Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis

Low Teck Yew, Sebastiaan vanHeesch, Henk vandenToorn, Piero Giansanti, Alba Cristobal, Pim Toonen, Sebastian Schafer, Norbert Hübner, Bas vanBreukelen, Shabaz Mohammed, Edwin Cuppen, Albert J.R. Heck, Victor Guryev

Research output: Contribution to journalArticle

78 Citations (Scopus)

Abstract

Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 26,463 rat liver proteins. We validated 1,195 gene predictions, 83 splice events, 126 proteins with nonsynonymous variants, and 20 isoforms with nonsynonymous RNA editing. Quantitative RNA sequencing and proteomics data correlate highly between strains but poorly among each other, indicating extensive nongenetic regulation. Our multilevel analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in genome-wide association studies for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner.

Original languageEnglish
Pages (from-to)1469-1478
Number of pages10
JournalCell Reports
Volume5
Issue number5
DOIs
Publication statusPublished - 12 Dec 2013
Externally publishedYes

Fingerprint

Proteome
Genomics
Proteomics
Rats
Genes
Liver
RNA
RNA Editing
Hypertension
RNA Sequence Analysis
Multilevel Analysis
Proteins
Genome-Wide Association Study
Gene Expression Profiling
Inbred SHR Rats
Molecular Dynamics Simulation
Molecular dynamics
Protein Isoforms
Association reactions
Tissue

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. / Teck Yew, Low; vanHeesch, Sebastiaan; vandenToorn, Henk; Giansanti, Piero; Cristobal, Alba; Toonen, Pim; Schafer, Sebastian; Hübner, Norbert; vanBreukelen, Bas; Mohammed, Shabaz; Cuppen, Edwin; Heck, Albert J.R.; Guryev, Victor.

In: Cell Reports, Vol. 5, No. 5, 12.12.2013, p. 1469-1478.

Research output: Contribution to journalArticle

Teck Yew, L, vanHeesch, S, vandenToorn, H, Giansanti, P, Cristobal, A, Toonen, P, Schafer, S, Hübner, N, vanBreukelen, B, Mohammed, S, Cuppen, E, Heck, AJR & Guryev, V 2013, 'Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis', Cell Reports, vol. 5, no. 5, pp. 1469-1478. https://doi.org/10.1016/j.celrep.2013.10.041
Teck Yew, Low ; vanHeesch, Sebastiaan ; vandenToorn, Henk ; Giansanti, Piero ; Cristobal, Alba ; Toonen, Pim ; Schafer, Sebastian ; Hübner, Norbert ; vanBreukelen, Bas ; Mohammed, Shabaz ; Cuppen, Edwin ; Heck, Albert J.R. ; Guryev, Victor. / Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. In: Cell Reports. 2013 ; Vol. 5, No. 5. pp. 1469-1478.
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